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- DNAseq Assembly in Velvet
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- Mapping With BWA and Bowtie
- Orthology Assignment
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Bench Work
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- Protocols
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Basic Unix tools and commands
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- Archived and Compressed Files
- Killing Processes
- Unix Commands
- Editing text files
- Installing Programs
Job control and useful trickery for writing your own pipelines
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- IO Redirection
- Running Long Jobs
The basics of working remotely
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- Computing Resources on Campus
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Analysis Tools
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- BLAST
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Cloud Computing with Amazon
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- Amazon EC2 Security groups
- Cloud computing at Amazon
- The Most Bang for Your Buck
Tutorials
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- Analyzing Barcode Data in SPIDER
- Calling SNPs in Next-gen Data
- DNAseq Assembly in Velvet
- Getting Started With Your Data
- Orthology Assignment
- RNAseq Assembly in Trinity
- Setting up an FTP server on a Mac
- DESeq
- Differential Gene Expression Python Pipeline
- edgeR
- Mapping With BWA and Bowtie